Stock composition of adult chum salmon Oncorhynchus keta caught in a setnet fishery estimated using genetic identification, scale patterns, and otolith thermal marking

Abstract

Three different techniques for stock identification, namely scale patterns, otolith thermal marks, and single-nucleotide polymorphism (SNP) markers, were applied to the same mixture samples of chum salmon collected in a setnet fishery in the Sea of Okhotsk, off Hokkaido, Japan, to evaluate consistency and accuracy among the techniques. The scale pattern and SNP analyses provided similar estimates for two regional origins (Hokkaido and Honshu) with data for 2011-2013; for each year, the Hokkaido-origin stock was dominant in September and early October, but the Honshu-origin stock was dominant by late October. The SNP analysis specified five geographical origins of chum salmon (the Okhotsk coast, Hokkaido and Honshu coasts of the Sea of Japan, and Hokkaido and Honshu coasts of the Pacific), whereas the other techniques did not identify multi-regional origins. Recaptures of otolith-marked chum salmon were used for estimating the proportions of fish originating from the Hokkaido Sea of Japan region; these estimates differed from those based on the SNP analysis. This study demonstrated that scale pattern and SNP analyses have the potential to provide nearly consistent estimates for the two regional origins, and can possibly help us to understand the interception of migrating chum salmon in Japan.

Population structure of chum salmon and selection on the markers collected for stock identification

“…The population structure of chum salmon has also been studied extensively using various markers, such as isozymes (Kijima & Fujio, 1979 ; Okazaki, 1982 ; Sato & Urawa, 2015 ; Seeb & Crane, 1999 ; Seeb et al., 1995 ; Wilmot et al., 1994 ; Winans et al., 1994 ), mitochondrial DNA (mtDNA) (Garvin et al., 2010 ; Park et al., 1993 ; Sato et al., 2004 ; Yoon et al., 2008 ), minisatellites (Taylor et al., 1994 ), and microsatellites (Beacham, Sato, et al., 2008 ; Beacham, Varnavskaya, et al., 2008 ; Beacham, Candy, Le, et al., 2009 ; Beacham, Candy, Wallace, et al., 2009 ; Olsen et al., 2008 . More recently, SNPs were developed to improve accuracy of mixed‐stock identification and have also been used for population genetics (Garvin et al., 2013 ; Petrou et al., 2014 ; Saito et al., 2020 ; Sato et al., 2014 ; Seeb et al., 2011 ; Small et al., 2015 ). A high‐throughput panel was developed for chum salmon, and patterns of linkage disequilibrium have been examined (McKinney et al., 2020 ).…”

“…International sampling of chum salmon has been conducted cooperatively across its distribution range to establish baseline genotype data for effective GSI Beacham, Candy, Wallace, et al, 2009;Beacham, Sato, et al, 2008;Beacham, Varnavskaya, et al, 2008;Seeb & Crane, 1999;Seeb et al, 1995;Urawa et al, 2005Urawa et al, , 2009Wilmot et al, 1994). The population structure of chum salmon has also been studied extensively using various markers, such as isozymes (Kijima & Fujio, 1979;Okazaki, 1982;Sato & Urawa, 2015;Seeb & Crane, 1999;Seeb et al, 1995;Wilmot et al, 1994;Winans et al, 1994), mitochondrial DNA (mtDNA) (Garvin et al, 2010;Park et al, 1993;Sato et al, 2004;Yoon et al, 2008), minisatellites (Taylor et al, 1994), and microsatellites (Beacham, Sato, et al, 2008;Beacham, Varnavskaya, et al, 2008;Beacham, Candy, Wallace, et al, 2009;Olsen et al, 2008. More recently, SNPs were developed to improve accuracy of mixed-stock identification and have also been used for population genetics (Garvin et al, 2013;Petrou et al, 2014;Saito et al, 2020;Sato et al, 2014;Seeb et al, 2011;Small et al, 2015). A high-throughput panel was developed for chum salmon, and patterns of linkage disequilibrium have been examined (McKinney et al, 2020).…”

Population structure of chum salmon and selection on the markers collected for stock identification

“…The population structure of chum salmon has also been studied extensively using various markers, such as isozymes (Kijima & Fujio, 1979; Okazaki, 1982; Sato & Urawa, 2015; Seeb & Crane, 1999; Seeb et al, 1995; Wilmot et al, 1994; Winans et al, 1994), mitochondrial DNA (mtDNA) (Garvin et al, 2010; Park et al, 1993; Sato et al, 2004; Yoon et al, 2008), minisatellites (Taylor et al, 1994), and microsatellites (Beacham et al, 2008a,b, 2009a,b; Olsen et al, 2008. More recently, SNPs were developed for accurate stock identification and have also been used for population genetics (Garvin et al, 2013; Petrou et al, 2014; Saito et al, 2020; Sato et al, 2014; Seeb et al, 2011; Small et al, 2015). A high-throughput panel was developed for chum salmon and patterns of linkage disequilibrium have been examined (McKinney et al, 2020).…”

Hatchery release programme modified the genetic diversity and population structure of wild Chinese sucker (Myxocyprinus asiaticus) in the upper Yangtze River

“…There are 52 power stations generating more than 1 million kilowatts, and 107 power stations generating more than 300,000 kilowatts, as well as many medium and small hydropower stations that have been built or are under construction (He et al, 2011;Chu, Liu & Pan, 2019). Its plastic tags, otolith marking (Saito et al, 2020), coded wires (Simon & Wickström, 2020), fluorescent elastomer tags, visible alphanumeric plastic tags or passive integrated transponders (Hanson et al, 2020), as well as heritable genetic marks such as mitochondrial DNA, minisatellites, microsatellites, transcribed sequences, anonymous cDNA or random amplified polymorphic DNAs (Gharrett et al, 2001;Hsu et al, 2020) before release should be seriously considered. It is better to identify the hatchery of origin for fish captured in the wild during the monitoring programme, hence the suggestion of 'familyprinting' for released M. asiaticus (Letcher & King, 1999).…”